Updates
Model and report changes
- Over January 2022 our model has been redesigned to incorporate the booster vaccination campaign and to be able to capture, in an unbiased way, the ecological effects of the emergence and subsequent dominance of the Omicron variant. In particular, we have stratified the entire model by vaccination status so that we can more accurately capture the impacts of waning immunity. The duration of immunity following infection is assumed to have a mean of around 18 months, but this falls rapidly around the time of the emergence of omicron to account for the immune escape of this variant. The waning of vaccine-derived immunity is captured through an assumed drop in vaccine efficacy at this time.
- A further modification to the model has been required due to the scaling back of the testing programme. Since March 2020 we have been calibrating the model against reported deaths within sixty days of a positive test. We now report the results from a model that uses data on new diagnoses in hospitals (where testing is still routine). The structure of the model remains similar but we make new assumptions about the proportion of infections that are detected by hospital-based testing, and the time taken post-infection for this detection to occur.
- We have extended the use of serological data to use samples taken beyond the first wave of the pandemic. The samples are those collected by NHS Blood and Transplant using the Roche-N assay, which measures the prevalence of infection-acquired antibodies in the population.
- The model also accounts for a different susceptibility to infection in each adult age group (no prior information is used); and for the under-15s, (using prior information from Viner et al, 2020, which estimates children to be less likely to acquire infection when in contact with an infectious individual).
- The model has the ability to incorporate estimates of community prevalence, by region and age group, from the Office of National Statistics COVID-19 Infection /Survey (ONS CIS; see Data Sources for details). These are included weekly since the outset of the Survey in May 2020 for the age groups >4 years to provide a more timely source of information on recent trends in incidence.
- The underlying probability of an unvaccinated individual testing positive in hospital following infection with SARS-CoV2 (the apparent infection-hospitalisation rate, IHR) is allowed to change gradually over the course of 30 days every (approximately) 100 days. This is designed to reflect fluctuations due to seasonal effects, demand on healthcare services or the emergence of new virus variants of differing severity.
- The “Epidemic summary” only reports the current value for the IHR by age. To visualise how this has changed over time in our model, see the IHR tab in the ‘Infections and Deaths’ section of the report. The quantity that is now plotted under this tab is the probability of being diagnosed in hospital if infected, taking into account the impact of the immunisation programme - it is an average of a lower rate of hospitalisation among vaccinated individuals and a higher rate among the unvaccinated.
- The attack rate table shows the proportion of individuals to have ever been infected over the course of the pandemic. Under any “Infections” tab, what is presented is the totality of all infections, including reinfections, and will therefore show values higher than the attack rate might suggest.
Data changes
- Data on new diagnoses in hospital testing. This is a composite dataset derived from two sources
- February–October 2020: The NHS England Secondary Uses Service (SUS) dataset, a collection of complete, accurate information on all hospitalisations with and due to COVID-19 infection. This is a comprehensive dataset but lacks the timeliness required for real-time surveillance, as individual records are completed for an individual and recorded on the system only upon death or hospital discharge.
- October 2020 onwards: NHS England and NHS Improvement COVID-19 Hospital Daily Situation Reports. Prior to this date, the NHS Situation Reports did not have the age-group granularity required by the model.
Updated findings
- The estimated number of new daily infections on 17th June across England has increased significantly to 169,000 (139,000–212,000, 95% credible interval). The daily infection rate is estimated to be 302 per 100k population per day nationally. The highest rate is currently in the South West (SW) with 426 infections per 100K population. The next highest rates are to be found in the South East (SE), West Midlands (WM) and North East (NE) with 368, 335 and 307 infections per 100K population, all above the national average. London (GL), and Yorkshire and the Humber (YH) have infection rates of 273 and 260 per 100k, whilst the lowest rates are in the North West (NW), East of England (EE) and East Midlands (EM) though all are above 200 infections per 100k. Note that a substantial proportion of these infections will be asymptomatic.
- The model predictions for the daily number of new diagnoses in hospitals reached a low of 451 diagnoses per day around May 27th and has since started increasing, currently doubling in number every 19.4 days across the country. We forecast that by July 8th, there will be 1,000 to 1,800 new diagnoses in hospitals per day.
- This week we believe the national Rt to be greater than 1. In most regions Rt is not estimated to be greater than one with certainty, but in SE, SW and WM, as well as for England as a whole, the possibility that Rt < 1 can be excluded..
- The growth rate for England is 0.04 (0.03– -0.06) per day. This means that, nationally, the number of infections is increasing, corresponding to an Rt of around 1.4.
- Our estimates for the attack rate, that is the proportion of the regional populations who have ever been infected, is 81.4% nationwide, and exceeds 80% in almost all regions except NW, EM, SE and EE. However, the estimated total number of infections to date (64.2m) far exceeds the size of the population of England.
- Note that the hospitalised diagnosis data used are only partially informative on Rt over the last two weeks. Therefore, the estimate for current incidence, Rt and the forecast of daily numbers of deaths are likely to be subject to significant revision.
Interpretation
Across England, we estimate that the daily number of diagnoses in hospitals are once again on the increase. Estimates for PCR-positive infection prevalence are similarly increasing, in all ONS regions and in all age groups. Despite the high rates of infection over the Omicron waves, continued waning of immunity and the increasing presence of the BA.4 and BA.5 sub-strains are sustaining an Rt that is currently around 1.4. Overall, since Dec 1st 2021, the Omicron variant has taken the cumulative number of infections from 26.2 million individuals to 64.2 million. Over 30% of all infections now are re-infections and this fraction will continue to increase. The fall in the estimated age-specific IHR since December 2021 indicates that infection with the Omicron variant is less likely to result in a diagnosis in hospital.This oOmicron-era decline represents a fall of over 50% with the most steep decline in IHR in the 45-64 and 65-74 age groups. After March the overall IHR has increased, indicative of a gradual shift in COVID infections towards older age groups, though this has stabilised since May. Currently the overall IHR is 0.67% (0.65%–0.68%), highest in the over-75s at 3.4% (3.3%–3.5%).
Summary
Real-time tracking of an epidemic, as data accumulate over time, is an essential component of a public health response to a new outbreak. A team of statistical modellers at the MRC Biostatistics Unit (BSU), University of Cambridge, are working to provide regular now-casts and forecasts of COVID-19 infections and deaths. This information feeds directly to the SAGE sub-group, Scientific Pandemic Influenza sub-group on Modelling (SPI-M), and to regional Public Health England (PHE) teams.
Methods
We fit a transmission model (Birrell et al. 2020) to a number of data sources (see ‘Data Sources’), to reconstruct the number of new COVID-19 infections over time in different age groups and NHS regions, estimate a measure of ongoing transmission and predict the number of new COVID-19 deaths.
Data sources
We use:
- Data on COVID-19 confirmed deaths from the Public Health England (PHE) line-listing This consists of a combination of deaths notified to:
- the Demographics Batch Service (DBS), a mechanism that allows PHE to submit a file of patient information to the National Health Service spine for tracing against the personal demographics service (PDS). PHE submit a line list of patients diagnosed with COVID-19 to DBS daily. The file is returned with a death flag and date of death updated (started 20th March, 2020).
- NHS England, who report data from NHS trusts relating to patients who have died after admission to hospital or within emergency department settings.
- Health Protection Teams (HPTs), resulting from a select survey created by PHE to capture deaths occurring outside of hospital settings, e.g. care homes (started 23rd March, 2020)
- Data on antibody prevalence in blood samples from a PHE survey of NHS Blood Transfusion (NHSBT) donors.
Data are stratified into eight age groups: <1, 1-4, 5-14, 15-24, 25-44, 45-64, 65-74, 75+, and the NHS England regions (North East and Yorkshire, North West, Midlands, East of England, London, South East, South West).
- Published information on the the natural history of COVID-19 (Verity et al., 2020; Li et al, 2020)
- Information on contacts between different age groups from:
- A Survey that describes relative rates of contacts between different age groups (Mossong et al. 2008).
- Google Community Mobility reports, informing the changes in people’s mobility over the course of the pandemic, particularly after the March 23rd lockdown measures.
- The ONS’ time use survey, which in conjunction with the google mobility study, allows estimation of the changing exposure to infection risk over time.
- Data from the Department for Education describing the proportion of children currently attending school.
- Daily data on the numbers of people getting immunised by age-group and region. These data are derived from the National Immunisation Management Service (NIMS). These data includes all COVID-19 immunisations administered at hospital hubs, local immunisation service sites such as GP practices, and dedicated immunisation centres.
- Data on new diagnoses in hospital testing. This is a composite dataset derived from two sources
- February-October 2020: The NHS England Secondary Uses Service (SUS) dataset, a collection of complete, accurate information on all hospitalisations with and due to COVID-19 infection. This is a comprehensive dataset but lacks the timeliness required for real-time surveillance, as individual records are completed for an individual and recorded on the system only upon death or hospital discharge.
- October 2020 onwards: NHS England and NHS Improvement COVID-19 Hospital Daily Situation Reports. Prior to this date, the NHS Situation Reports did not have the age-group granularity required by the model.
Epidemic summary
Current \(R_t\)
Value of \(R_t\), the average number of secondary infections due to a typical infection today.
Attack rate
The percentage of a given group that has been infected.
Change in infections incidence
Growth rates
NB: negative growth rates are rates of decline. Values are daily changes.
| England |
0.04 |
0.03 |
0.06 |
| East of England |
0.03 |
-0.01 |
0.06 |
| East Midlands |
0.03 |
-0.01 |
0.07 |
| London |
0.02 |
-0.01 |
0.06 |
| North East |
0.02 |
-0.02 |
0.05 |
| North West |
0.01 |
-0.04 |
0.05 |
| South East |
0.05 |
0.02 |
0.08 |
| South West |
0.06 |
0.03 |
0.09 |
| West Midlands |
0.04 |
0.01 |
0.08 |
| Yorkshire and The Humber |
0.03 |
-0.01 |
0.06 |
Halving times
Halving times in days, if a region shows growth than value will be NA.
| England |
NA |
NA |
NA |
| East of England |
NA |
46.93 |
NA |
| East Midlands |
NA |
50.85 |
NA |
| London |
NA |
126.34 |
NA |
| North East |
NA |
38.51 |
NA |
| North West |
NA |
16.41 |
NA |
| South East |
NA |
NA |
NA |
| South West |
NA |
NA |
NA |
| West Midlands |
NA |
NA |
NA |
| Yorkshire and The Humber |
NA |
76.79 |
NA |
Doubling times
Doubling times in days, if a region shows decline then the value will be NA.
| England |
16.82 |
11.83 |
25.82 |
| East of England |
26.28 |
11.72 |
NA |
| East Midlands |
26.04 |
10.60 |
NA |
| London |
29.56 |
11.15 |
NA |
| North East |
43.81 |
13.83 |
NA |
| North West |
90.16 |
14.08 |
NA |
| South East |
13.59 |
8.35 |
41.93 |
| South West |
11.42 |
7.50 |
23.55 |
| West Midlands |
16.56 |
9.06 |
101.21 |
| Yorkshire and The Humber |
22.68 |
11.65 |
NA |
Change in admissions incidence
Growth rates
NB: negative growth rates are rates of decline. Values are daily changes.
| England |
0.04 |
0.02 |
0.05 |
| East of England |
0.02 |
-0.01 |
0.06 |
| East Midlands |
0.02 |
-0.01 |
0.06 |
| London |
0.02 |
0.00 |
0.06 |
| North East |
0.02 |
-0.02 |
0.05 |
| North West |
0.01 |
-0.02 |
0.06 |
| South East |
0.05 |
0.02 |
0.09 |
| South West |
0.06 |
0.03 |
0.10 |
| West Midlands |
0.04 |
0.00 |
0.08 |
| Yorkshire and The Humber |
0.03 |
0.00 |
0.06 |
Halving times
Halving times in days, if a region shows growth than value will be NA.
| England |
NA |
NA |
NA |
| East of England |
NA |
83.95 |
NA |
| East Midlands |
NA |
69.13 |
NA |
| London |
NA |
2145.90 |
NA |
| North East |
NA |
44.96 |
NA |
| North West |
NA |
30.78 |
NA |
| South East |
NA |
NA |
NA |
| South West |
NA |
NA |
NA |
| West Midlands |
NA |
NA |
NA |
| Yorkshire and The Humber |
NA |
306.62 |
NA |
Doubling times
Doubling times in days, if a region shows decline then the value will be NA.
| England |
19.41 |
13.79 |
28.87 |
| East of England |
28.91 |
11.53 |
NA |
| East Midlands |
28.85 |
10.77 |
NA |
| London |
30.04 |
10.90 |
NA |
| North East |
40.36 |
12.95 |
NA |
| North West |
51.57 |
12.24 |
NA |
| South East |
13.72 |
7.90 |
40.95 |
| South West |
11.42 |
6.95 |
27.53 |
| West Midlands |
17.29 |
8.71 |
212.28 |
| Yorkshire and The Humber |
22.97 |
11.24 |
NA |
## The execution of the prevalence code block will proceed if
## prev.dat exists and this is TRUE
## it is not an external report and this is FALSE
Infections and deaths
The shaded areas show periods of national lockdown, the green lines the dates (once confirmed) of the steps in the roadmap in the UK Governement’s COVID-19 Response – Spring 2021, and the red line shows the date these results were produced (17 Jun).